GEO DataSets

(Submitter supplied) Biofilm lifestyle is critical for bacterial pathogens to colonize and protect themselves from host immunity and antimicrobial chemicals in plants and animals. The formation and regulation mechanism of phytobacterial biofilm are still obscure. Here, we found that Ralstonia solanacearum Resistance to ultraviolet C (RuvC) is highly abundant in biofilm and positively regulates pathogenicity by governing systemic movement in tomato xylem. more...

Organism:

Ralstonia solanacearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34644

6 Samples

Download data: TXT

(Submitter supplied) The cadmium-resistant Cupriavidus sp. E324 strain has been previously shown to have a high potential for use in cadmium (Cd) remediation, due to its high capacity for cadmium bioaccumulation. According to the comparative genomic analysis, the E324 strain was most closely related to C. nantongensis X1 T , indicating that the E324 strain should be re-identified as C. nantongensis. To unravel the Cd tolerance mechanisms of C. more...

Organism:

Cupriavidus nantongensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34734

6 Samples

Download data: TXT

(Submitter supplied) RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns of B. glumae BGR1 under infected rice panicle tissue.

Organism:

Burkholderia glumae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27527

3 Samples

Download data: TXT

(Submitter supplied) In this study we compare logarithmically grown Burkholderia thailadensis wildtype to a transposon mutant that is disrupted in gshA1, or gshA2, which are involved in glutathione biosynthesis or egtB, involved in ergothioneine biosynthesis using RNASeq to identify novel pathways where glutathione or ergothioneine may be involved.

Organism:

Burkholderia thailandensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33677

8 Samples

Download data: CSV, XLSX

(Submitter supplied) Plant pathogens require lethal virulence factors, susceptible hosts, and optimal environmental conditions for disease establishment. High soil salinity, exacerbated by climate change, significantly impacts agro-biological ecosystems. However, the overall interactions between plant pathogens and salt stress are not fully characterized or understood. This study examines the effects of salt stress on representative plant pathogens: Burkholderia gladioli, Pectobacterium carotovorum subsp. more...

Organism:

Ralstonia solanacearum; Burkholderia gladioli; Pectobacterium carotovorum subsp. carotovorum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34740 GPL29295 GPL34741

18 Samples

Download data: TXT

(Submitter supplied) We identified BP1026b_II1561 to be an important transcriptional regulator controling late stages of intracellular infection. RNA-seq analysis was performed to further investigate the regulatory network of II1561 regulation. ChIP-seq was also performed under the same conditions.

Organism:

Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32930

2 Samples

Download data: XLSX

(Submitter supplied) We identified BP1026b_II1561 to be an important transcriptional regulator controling late stages of intracellular infection. RNA-seq analysis was performed to further investigate the regulatory network of II1561 regulation. ChIP-seq was also performed under the same conditions.

Organism:

Burkholderia pseudomallei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32930

2 Samples

Download data: XLSX

(Submitter supplied) The classical bordetellae (Bordetella pertussis, B. parapertussis, and B. bronchiseptica) are obligate aerobes that use only oxygen as their terminal electron acceptor for electron transport-coupled oxidative phosphorylation. Therefore, access to oxygen is critical for these bacteria to survive. To better understand how B. bronchiseptica changes its gene regulation when faced with different levels of oxygen, we grew liquid cultures of B. more...

Organism:

Bordetella bronchiseptica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34533

12 Samples

Download data: TSV

(Submitter supplied) Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological solution to promote plants growth in prospective extraterrestrial human outposts. In this study, we investigated the adaptation of the legume symbiont Paraburkholderia phymatum to simulated microgravity (s0-g) at the transcriptome level by performing an RNA-Seq analysis. The results revealed a drastic effect on gene expression, with roughly 23 % of P. more...

Organism:

Paraburkholderia phymatum STM815

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22728

6 Samples

Download data: TXT

(Submitter supplied) The goals of this study were to determine differential gene expression between Achromobacter xylosoxidans clinical isolate Ax 7 in a synthetic artificial sputum media compared to a rich media control (LB).

Organism:

Achromobacter xylosoxidans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33525

6 Samples

Download data: CSV, TXT

(Submitter supplied) Bacterial pathogens exhibit a remarkable ability to persist and thrive in diverse ecological niches. Understanding the mechanisms enabling their transition between environments is crucial to control dissemination and potential disease outbreaks. Here, we use Ralstonia solanacearum, the causing agent of the bacterial wilt disease, as a model to investigate the bacterial transcriptomic adaptation to two environments, water and soil, and compare it with the well-studied in planta gene expression. more...

Organism:

Ralstonia solanacearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33632

6 Samples

Download data: CSV, XLSX

(Submitter supplied) Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging approach to remove PCBs from sediment, but development of aerobic biofilms on BC for long-term, sustained LC-PCBs remediation is poorly understood. This work aimed to characterize cell enrichment and activity of biphenyl- and benzoate-grown Paraburkholderia xenovorans strain LB400 on various BCs. more...

Organism:

Paraburkholderia xenovorans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33884

12 Samples

Download data: XLSX

(Submitter supplied) To investigate the molecular mechanisms of how Cupriavidus basilensis SRS may aid bioextraction of metals from ores, we exposed C. basilensis SRS to different metals, as well as natural ores

Organism:

Cupriavidus basilensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32789

10 Samples

Download data: TXT

(Submitter supplied) To comprehend the underlying mechanisms of NSC proliferation and differentiation, microRNA expression was investigated. Total RNA was extracted from NSCs, ESCs, and MEFs, and microRNA expression was examined using RT-PCR. This was accomplished utilizing the System Biosciences' Mouse miRNome Sanger miRVase microRNA Profiler Set.

Organism:

Bordetella pertussis; Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL29570

3 Samples

Download data: XLSX

(Submitter supplied) A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intended to mimic industrial processes.

Organism:

Bordetella pertussis Tohama I

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32624

21 Samples

Download data: XLSX

(Submitter supplied) We identified BP1026b_II1046 (SapR) to be an important transcriptional regulator controling surface attachment factor 1 (sap1). RNA-seq analysis was performed to further investigate the regulatory network of SapR regulation.

Organism:

Burkholderia pseudomallei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32930

6 Samples

Download data: XLSX

(Submitter supplied) To verify genes that are directly regulated by BysR, we used DNA affinity purification sequencing analysis (DAP-seq) for genome-wide recognition of BysR binding sites in vitro. The HALO-fusion BysR protein was successfully expressed and purified. After affinity purification and sequencing, at least 22 million double-end reads per sample were generated and with > 99 % of reads uniquely mapped to the JP2-270 genome. more...

Organism:

Burkholderia sp. JP2-270

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL31243

3 Samples

Download data: FA, TXT, WIG

(Submitter supplied) Purpose: In order to identify the differentially expressed genes between wild type and ΔbysR, we performed RNA-seq analysis.Methods：All the isolates were cultured in CM medium for 24 h at 28℃. Three repetitions were performed for each treatment. The samples were sequenced on an Illumina Hiseq 2000 platform.Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. more...

Organism:

Burkholderia sp. JP2-270

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31232

6 Samples

Download data: TXT

(Submitter supplied) Widely reported discrepancies between metabolic flux and transcripts or enzyme levels in bacterial metabolism imply complex regulation mechanisms need to be considered, especially in new bacterial platforms for bioremediation and bioproduction. Comamonas testosteroni strains, which metabolize various natural and xenobiotic aromatic compounds, represent such platforms whose metabolic regulations are still unknown. more...

Organism:

Comamonas testosteroni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31156

12 Samples

Download data: TSV

(Submitter supplied) Poly(ethylene terephthalate) (PET)-degrading bacterium Ideonella sakaiensis produces hydrolytic enzymes that convert PET, via mono(2-hydroxyethyl) terephthalate (MHET), into the monomeric compounds, terephthalic acid (TPA) and ethylene glycol (EG). Understanding PET metabolism is critical if this bacterium is to be engineered for bioremediation and biorecycling. TPA uptake and catabolism in I. sakaiensis have previously been studied, but EG metabolism remains largely unexplored despite its importance. more...

Organism:

Piscinibacter sakaiensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32339

3 Samples

Download data: TXT